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If you understand the USB Blaster protocol, you can also combine both methods, perform generic JTAG through USB Blaster. It may be interesting for accessing other vendors devices in the JTAG chain or boundary scan tests of Altera devices through an existing USB Blaster.
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That would definitely be my goal.. have the Altera FPGA support the ByteBlaster protocol so that any JTAG devices that hang off of it may be programmed via the Quartus software. I use Quartus/USB-Blaster in Windows, but isn't there an (open-source) Linux version?
Doing some poking around, it seems the USB Protocol was once posted, but has since been taken down
(
http://wiki.openchip.org/index.php/altera_usb_blaster http://wiki.openchip.org/index.php/altera_bitblaster )
On the bright side, there appears to be one project that might have already done this before, or at least come to close..
http://www.ixo.de/info/usb_jtag/
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